def perform_sims(config, dirstub, num):
for i in range(num):
i += 1
ttr = TreeToReads(configfi=config, run=0)
diri = "{}{}".format(dirstub, i)
if not os.path.exists(diri):
os.makedirs(diri)
ttr.outd = diri
ttr.run_art()
exp_tree = dendropy.Tree.get_from_path(expected,
"newick",
taxon_set=taxon_namespace)
est_tree = dendropy.Tree.get_from_path(estimated,
"nexus",
taxon_set=taxon_namespace)
return (est_tree.symmetric_difference(exp_tree))
if __name__ == '__main__':
ttr = TreeToReads(
configfi=
'/home/ejmctavish/Documents/FDA/TreetoReads/tests/input/tree_from_fasta.cfg',
run=0)
print("outd is {}".format(ttr.outd))
ttr.outd = "/home/ejmctavish/Documents/FDA/TreetoReads/tests/tree_from_fasta"
ttr.makeOut()
ttr.mutGenomes()
print(ttr.getArg('genome'))
# enter the directory like this:
os.system("cat {}/fasta_files/*.fasta > {}/mini.aln".format(
ttr.outd, ttr.outd))
os.system("Garli tests/garli_mini.conf > {}/garliout".format(ttr.outd))
assert (compare_trees('tests/input/simple_expected.tre',
'tests/tree_from_fasta/tff.best.tre') == 0)
assert (compare_trees('tests/input/alt.tre',
'tests/tree_from_fasta/tff.best.tre') != 0)
print('Topology is correct')
os.system(
"rm -r /home/ejmctavish/Documents/FDA/TreetoReads/tests/tree_from_fasta"
)
import unittest
from treetoreads import TreeToReads
import subprocess
import dendropy
import subprocess
import os
def compare_trees(expected, estimated):
# assert(estimated.euclidean_distance(expected)<= branch lengths are hard to test. TODO figure out how.
taxon_namespace = dendropy.TaxonSet()
exp_tree = dendropy.Tree.get_from_path(expected, "newick", taxon_set=taxon_namespace)
est_tree = dendropy.Tree.get_from_path(estimated, "nexus", taxon_set=taxon_namespace)
return est_tree.symmetric_difference(exp_tree)
if __name__ == "__main__":
ttr = TreeToReads(configfi="/home/ejmctavish/Documents/FDA/TreetoReads/tests/input/tree_from_fasta.cfg", run=0)
print("outd is {}".format(ttr.outd))
ttr.outd = "/home/ejmctavish/Documents/FDA/TreetoReads/tests/tree_from_fasta"
ttr.makeOut()
ttr.mutGenomes()
print(ttr.getArg("genome"))
# enter the directory like this:
os.system("cat {}/fasta_files/*.fasta > {}/mini.aln".format(ttr.outd, ttr.outd))
os.system("Garli tests/garli_mini.conf > {}/garliout".format(ttr.outd))
assert compare_trees("tests/input/simple_expected.tre", "tests/tree_from_fasta/tff.best.tre") == 0
assert compare_trees("tests/input/alt.tre", "tests/tree_from_fasta/tff.best.tre") != 0
print("Topology is correct")
os.system("rm -r /home/ejmctavish/Documents/FDA/TreetoReads/tests/tree_from_fasta")
